Business and Biopdiversity - Ch 2 - Snowball

Setup

Code

#|

# library(bibtex)
library(openalexR)

Thank you for using openalexR!
To acknowledge our work, please cite the package by calling
`citation("openalexR")`.

Code

library(IPBES.R)

library(tibble)
library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Code

# library(writexl)
# library(ggplot2)
# library(ggraph)
# library(tidygraph)

library(knitr)

list.files(
    "R",
    full.names = TRUE,
    recursive = TRUE
) |>
    sapply(
        FUN <- source
    )

named list()

Code

kp <- read.csv(file.path("Key Papers", "Tuije.csv"))

Back to Readme

Simple Snowball

Setup OpelAnex usage and do snowball serarch

Code

#|


fn <- file.path(".", "data", "key_works.rds")
if (file.exists(fn)) {
    key_works <- readRDS(fn)
} else {
    key_works <- oa_fetch(
        entity = "works",
        doi = kp$DOI,
        verbose = FALSE
    )
    saveRDS(key_works, fn)
}

ids <- openalexR:::shorten_oaid(key_works$id)

fn <- file.path(".", "data", "snowball.rds")
if (file.exists(fn)) {
    snowball <- readRDS(fn)
} else {
    snowball <- oa_snowball(
        identifier = ids,
        verbose = FALSE
    )
    saveRDS(snowball, fn)
}

flat_snow <- snowball2df(snowball)  |>
 tibble::as_tibble()

Save snowball as Excel file (snowball_excel.xlsx)

TODO: not working - but why????

Code

fn <- file.path(".", "data", "snowball.xlsx")
if (!file.exists(fn)) {
    to_xlsx(
        snowball = snowball,
        xls_filename = fn
    )
}

The column are: (the Concept columns are not that relevant at the moment)

• id: internal id fromOpenAlex
• author: authors of the paper
• publication_year: publication year
• title: title of the paper
• doi: doi of the paper
• no_referenced_works: number of references in the paper which are also in OpenAlex
• cited_global: Number of times the paper has been cited
• cited_global_per_year: standardised number of times cirted (cited_global / number of years published)
• no_connections: number of connections in the rgaph, i.e. either cited or citing a paper in the snowball corpus
• concepts_l0: Concept 0. level assigned by OpenAlex
• concepts_l1: Concept 1. level assigned by OpenAlex
• concepts_l2: Concept 2. level assigned by OpenAlex
• concepts_l3: Concept 3. level assigned by OpenAlex
• concepts_l4: Concept 4. level assigned by OpenAlex
• concepts_l5: Concept 5. level assigned by OpenAlex
• author_institute: Institute of the authors
• institute_country: Country of the institute
• abstract: the abstract of the paper

Graph of links between references

Code

if (!file.exists(file.path("figures", "snowball_cited_by_count.png"))) {
plot_snowball(
    snowball,
    name = "snowball"
)
}

Snowball Cited by Count per Yeart

Supplemented Snowball by Edges between all Papers

We now supplement the citation network with the citations from the non-key papers, as these are not included in the previous network

Code

fn <- file.path("data", "snowball_supplemented.rds")
if (file.exists(fn)) {
    snowball_supplemented <- readRDS(fn)
} else {
    new_edges <- tibble(
        from = character(0),
        to = character(0)
    )

    works <- snowball$nodes$id

    for (i in 1:nrow(snowball$nodes)) {
        from <- works[[i]]
        to <- gsub("https://openalex.org/", "", snowball$nodes$referenced_works[[i]])
        to_in_works <- to[to %in% works]
        if (length(to_in_works) > 0) {
            new_edges <- add_row(
                new_edges,
                tibble(
                    from = from,
                    to = to_in_works
                )
            )
        }
    }

    snowball_supplemented <- snowball
    snowball_supplemented$edges <- add_row(snowball_supplemented$edges, new_edges) |>
        dplyr::distinct()
    saveRDS(snowball_supplemented, fn)
}

Code

if (!file.exists(file.path("figures", "snowball_supplemented_cited_by_count.png"))) {
    IPBES.R::plot_snowball(
        snowball_supplemented, 
        name = "snowball_supplemented", 
        path = "figures"
    )
}

Supplemented Cited by count